Download Identification of soil bacteria belonging to the phylum Acidobacteria

Identification of soil bacteria belonging to the phylum Acidobacteria
by MALDI-TOF mass spectrometry
Soares, C. E; Castro, V; Barreto, C; Magalhães, B. S.
Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia,
Universidade Católica de Brasília, DF, Brasil.
Recently, it has been shown that bacterial species of the phylum Acidobacteria
are abundant in Cerrado soil, representing more than 50% of total 16S rRNA
sequences obtained. These bacteria are expected to play an important role in
nutrient cycling in this Biome but are very difficult to obtain in culture. Using
novel culturing techniques, five Acidobacteria were isolated from soil samples
obtained near Cristalina, Goiás. These isolates were identified using 16S rRNA
gene phylogeny and characterized by colony and cell morphology. In addition,
MALDI-TOF MS has been applied to generate protein profiles of these isolates
that enabled the rapid differentiation of new Acidobacteria species. Two protein
extraction protocols were tested to optimize the amount of protein obtained.
Twenty mass spectra of each protein extract were acquired to ensure the
reproducibility of the MS profiles generated the mass range of spectra
acquisition was 2000 to 20000 m/z with a Microflex instrument (Bruker
Daltonics). Protein profiles were obtained and evaluated by principal component
analysis (PCA). These results were in good agreement with classical
phylogenetic analysis based upon rRNA 16S sequencing it was possible to
validate the application of this methodology for fast identification of species of
the Acidobacteria phylum and ensure the reproducibility of the mass spectra
obtained used to produce the phylogenetic tree. The use of MALDI-TOF MS for
the identification of soil bacteria is dependent upon the generation of a
database of protein profiles and these results constitute the first effort towards a
unified database for environmental soil bacteria.
Keywords: MALDI-TOF MS; Acidobacteria phylum; soil bacteria; Cerrado
Support: CNPq, Embrapa
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